Extremely underutilized mechanics are autonomy, overextension, and corruption.
Autonomy basically always ticks to 0 unless something interferes, most countries start with autonomy way too low already, and reduction of local autonomy isn't the huge headache it historically was. Your estates don't really feel any sort of way about local autonomy and historic privileges being revoked.
Overextension is only a problem immediately after conquest, before you can click the magic button to core a territory. Once cored, no matter where in the world it is, how many angry locals have to be governed, if you even have a land or sea connection to the province, what heathen or heretic religion they follow, there is never any issue with your administration being unable to properly govern.
Corruption is rarely a factor at all for any country. Even if it is you can just pay money to reduce it (lol), and the factors that do cause it: overextension, wrong-religion provinces, etc. are all very easy to avoid or temporary.
All three of these should tick towards an equilibrium based on your government, reforms, etc.
A mechanic that is utterly ahistorical (and for me, is an admission that EU4 is terrible at macro level country management) is colonial nations. De jure self-governing colonies quite simply did not exist for most of the game's timeline (only at the very end does it start to happen) and no strain is put on the central government for large bodies of overseas territory. Colonies being able to defend themselves is also fairly ahistorical (only big settler colonies were able to do so in any way.) You want to represent the de facto autonomy that many colonies had? If only there were some sort of mechanic to show a central government's limited control over an area...
They also completely neutered new world independence movements by making liberty desire such a joke to counter. You pretty much have to try to have a cn even attempt to revolt, let alone actually succeed.
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